Some 'civilian' Sealift Command vessels are armed; the Mars class combat stores ships had as many as six 3" guns mounted at one time or another.
And if one really desires to get technical- ALL U.S. Coast Guard ships were owned by the Department of the Treasury or the Department of Transportation until 2002. This means that they were not military vessels at all, but armed civilian law enforcement vessels- occasionally rather heavily armed ones at that!
I see little real difference here- if the vessel's operational crew was taken for the Reich's 'Coast Guard Equivalent,' then it could probably get away with being armed while still being 'civilian' in nature.
And how many of the MSCs or USGCs ships do you think make port calls that haven't been arranged at governmental level?
Who says this ship wouldn't prearrange it's ports-of-call in a similar manner?
I was unaware that any ship 'simply walked into Mordor' without some kind of advance approval. If a NOAA vessel is planning to stop in Japan, even though it's unarmed and crewed by civilians, it's still a foreign flag vessel and has ask the Japanese government for permission to enter harbor- right?